[English] 日本語
Yorodumi
- PDB-1oc3: HUMAN PEROXIREDOXIN 5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1oc3
TitleHUMAN PEROXIREDOXIN 5
ComponentsPEROXIREDOXIN 5
KeywordsOXIDOREDUCTASE / ANTIOXIDANT ENZYME / PEROXIREDOXIN / THIOREDOXIN PEROXIDASE / THIOREDOXIN FOLD / PEROXISOME / MITOCHONDRION / TRANSIT PEPTIDE
Function / homology
Function and homology information


peroxynitrite reductase activity / reactive nitrogen species metabolic process / negative regulation of transcription by RNA polymerase III / negative regulation of oxidoreductase activity / : / regulation of apoptosis involved in tissue homeostasis / RNA polymerase III transcription regulatory region sequence-specific DNA binding / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cysteine-type endopeptidase inhibitor activity involved in apoptotic process ...peroxynitrite reductase activity / reactive nitrogen species metabolic process / negative regulation of transcription by RNA polymerase III / negative regulation of oxidoreductase activity / : / regulation of apoptosis involved in tissue homeostasis / RNA polymerase III transcription regulatory region sequence-specific DNA binding / thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / Detoxification of Reactive Oxygen Species / antioxidant activity / peroxisomal matrix / positive regulation of collagen biosynthetic process / cell redox homeostasis / hydrogen peroxide catabolic process / cellular response to reactive oxygen species / TP53 Regulates Metabolic Genes / peroxidase activity / peroxisome / cellular response to oxidative stress / cytoplasmic vesicle / response to oxidative stress / mitochondrial matrix / inflammatory response / signaling receptor binding / intracellular membrane-bounded organelle / negative regulation of apoptotic process / perinuclear region of cytoplasm / mitochondrion / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Peroxiredoxin-5-like / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BENZOIC ACID / Peroxiredoxin-5, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsEvrard, C. / Declercq, J.-P.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Crystal Structure of a Dimeric Oxidized Form of Human Peroxiredoxin 5
Authors: Evrard, C. / Capron, A. / Marchand, C. / Clippe, A. / Wattiez, R. / Soumillion, P. / Knoops, B. / Declercq, J.-P.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: Crystal Structure of Human Peroxiredoxin 5, a Novel Type of Mammalian Peroxiredoxin at 1.5 A Resolution
Authors: Declercq, J.P. / Evrard, C. / Clippe, A. / Stricht, D.V. / Bernard, A. / Knoops, B.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: A Twinned Monoclinic Crystal Form of Human Peroxiredoxin 5 with Eight Molecules in the Asymmetric Unit
Authors: Declercq, J.P. / Evrard, C.
#3: Journal: J.Biol.Chem. / Year: 1999
Title: Cloning and Characterization of Aoeb166, a Novel Mammalian Antioxidant Enzyme of the Peroxiredoxin Family
Authors: Knoops, B. / Clippe, A. / Bogard, C. / Arsalane, K. / Wattiez, R. / Hermans, C. / Duconseille, E. / Falmagne, P. / Bernard, A.
History
DepositionFeb 5, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Oct 24, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.gene_src_strain ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PEROXIREDOXIN 5
B: PEROXIREDOXIN 5
C: PEROXIREDOXIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8265
Polymers54,5823
Non-polymers2442
Water1,11762
1
A: PEROXIREDOXIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3162
Polymers18,1941
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PEROXIREDOXIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3162
Polymers18,1941
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: PEROXIREDOXIN 5


Theoretical massNumber of molelcules
Total (without water)18,1941
Polymers18,1941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)79.195, 102.053, 145.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.2175, -0.9758, -0.0243), (0.9756, -0.2181, 0.0243), (-0.029, -0.0184, 0.9994)27.5035, 19.0982, 42.4959
2given(0.2436, -0.9699, 0.0053), (0.9699, 0.2436, 0.0004), (-0.0016, 0.0051, 1)26.5877, -20.1892, 30.4133

-
Components

#1: Protein PEROXIREDOXIN 5 / MITOCHONDRIAL PRECURSOR / PRX-V / PEROXISOMAL ANTIOXIDANT ENZYME / PLP / THIOREDOXIN PEROXIDASE ...MITOCHONDRIAL PRECURSOR / PRX-V / PEROXISOMAL ANTIOXIDANT ENZYME / PLP / THIOREDOXIN PEROXIDASE PMP20 / ANTIOXIDANT ENZYME B166 / AOEB166 / TPX TYPE VI / LIVER TISSUE 2D-PAGE SPOT 71B / ALU CO-REPRESSOR 1 / SBBI10


Mass: 18193.850 Da / Num. of mol.: 3 / Fragment: PEROXIREDOXIN 5, RESIDUES 54-214
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: LUNG / Plasmid: PQE-30 / Production host: ESCHERICHIA COLI M15 (bacteria) / References: UniProt: P30044
#2: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Compound detailsREDUCES HYDROGEN PEROXIDE AND HYDROPEROXIDES WITH REDUCING EQUIVALENTS USING THE THIOREDOXIN SYSTEM.
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57 %
Crystal growpH: 5.3
Details: PROTEIN WAS CRYSTALLIZED FROM 20% PEG 3350, 0.1 M SODIUM CITRATE BUFFER, PH 5.3, 1 MM DTT, 0.02 % (W/V) SODIUM AZIDE
Crystal grow
*PLUS
Temperature: 291 K / pH: 5.3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %(w/v)PEG33501reservoir
20.1 Msodium cirtate1reservoirpH5.3
31 mM1,4-dithio-DL-threitol1reservoir
40.02 %(w/v)sodium azide1reservoir
510 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8441
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 2002 / Details: PREMIRROR, BENT MIRROR
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8441 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 38821 / % possible obs: 96.9 % / Redundancy: 4.2 % / Rsym value: 0.047 / Net I/σ(I): 13.5
Reflection shellResolution: 2→2.2 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.332 / % possible all: 96.1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å / Num. measured all: 164737 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.05 Å / % possible obs: 95.2 %

-
Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HD2

1hd2


Resolution: 2→72.55 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.139 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1933 5 %RANDOM
Rwork0.221 ---
obs0.223 36850 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.93 Å2
Baniso -1Baniso -2Baniso -3
1-4.8 Å20 Å20 Å2
2---1.21 Å20 Å2
3----3.59 Å2
Refinement stepCycle: LAST / Resolution: 2→72.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3576 0 18 62 3656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223657
X-RAY DIFFRACTIONr_bond_other_d0.0010.023443
X-RAY DIFFRACTIONr_angle_refined_deg1.9451.9854944
X-RAY DIFFRACTIONr_angle_other_deg0.90138034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9633481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.81615655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1180.2571
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024094
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02676
X-RAY DIFFRACTIONr_nbd_refined0.2350.3766
X-RAY DIFFRACTIONr_nbd_other0.2160.33341
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.5218
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0960.53
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3970.323
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2450.380
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.56
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9131.52396
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55423825
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.73931261
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5044.51119
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.355 127
Rwork0.286 2654
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.14110.1133-0.97421.4356-0.4161.82170.14890.2075-0.0332-0.0785-0.0863-0.1409-0.17960.1513-0.06260.151-0.00450.02690.1153-0.01840.121312.1257.57526.519
21.193-0.28950.47792.8155-1.43812.7399-0.04580.12120.1268-0.3370.00920.01650.0806-0.06070.03660.0456-0.0557-0.03890.21160.04680.201716.75829.88668.488
32.0896-0.94570.5713.424-2.59172.8394-0.13560.05040.30520.28-0.0715-0.2475-0.53550.17060.20710.0931-0.03-0.020.23470.00750.195122.424-6.29857.043
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 161
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION2B1 - 161
4X-RAY DIFFRACTION2B201
5X-RAY DIFFRACTION3C1 - 161
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.9
LS refinement shell
*PLUS
Rfactor Rfree: 0.355 / Rfactor Rwork: 0.286

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more